Exploring the genetic features and signatures of selection in South China indigenous pigs

doi:10.1016/S2095-3119(20)63260-9

摘要/Abstract

摘要：

遗传特性的探索，可以了解群体内遗传结构，对探索群体形成提供有效信息。而选择信号检测不仅能反映选择对品种的培育作用，还有助于更好地理解选择机制。海南猪、五指山猪、两广小花猪是我国华南地区优秀的地方品种，具有耐粗饲、性成熟早、肉质鲜美等优点。杜洛克猪经历了长时间的正向选择，具有生长速度快、饲料转换率高、瘦肉率高等特点。本研究基于SNP（single-nucleotide polymorphism）芯片数据，对华南地区地方猪种及杜洛克猪6个群体，共计259个个体进行了主成分分析、系统发生树构建、群体结构分析、连锁不平衡分析、有效群体大小估计以及全基因组选择信号检测，旨在探究华南地区地方猪种的遗传特性与选择信号，为后续保种及利用提供一定参考信息。结果显示，6个猪群体被分为华南地区地方猪种和杜洛克猪两簇，而华南地区地方猪种簇中，海南地区地方猪种与两广小花猪分为两簇，此结果与主成分分析结果相似；5个华南地区地方猪种的有效群体大小在近年呈现迅速衰减趋势；当标记间距为100kb时，5个地方猪群体的连锁不平衡程度变化范围为：0.16-0.20，而杜洛克猪群体的连锁不平衡程度为0.32；此外，在华南地区地方猪种群体基因组中共检测到15个潜在受选择区域，在杜洛克猪基因组中检测到8个潜在受选择区域。综上所述，华南地区地方猪保种工作刻不容缓。群体结果分析和选择信号检测揭示了华南地区地方猪种不同群体间受选择方向的差异。本研究不仅为研究华南地区地方猪种的起源、有效群体大小和选择提供了新见解，并且还为日后该猪种的利用提供了参考信息。

Abstract:

To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism (SNP) BeadChips. Principal component analysis (PCA), effective population size (Ne), linkage disequilibrium (LD), and signatures of selection were explored and investigated among the six pig populations. The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago. The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population. However, the LD of all six pig populations showed the opposite order at long distances (>5 Mb). Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs. Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.

Key words: pigs , population structure , effective population size , SNP

. [J]. Journal of Integrative Agriculture, 2021, 20(5): 1359-1371.

DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe. Exploring the genetic features and signatures of selection in South China indigenous pigs[J]. Journal of Integrative Agriculture, 2021, 20(5): 1359-1371.

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